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<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>cudamapper</b></li><li class="navelem"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a></li>  </ul>
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<a href="#pub-attribs">Public Attributes</a> &#124;
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<div class="title">claragenomics::cudamapper::Overlap Struct Reference</div>  </div>
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<p><code>#include &lt;<a class="el" href="types_8hpp_source.html">types.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr class="memitem:a3d98a09e4ccd8bda66cb09a72adaf1fc"><td class="memItemLeft" align="right" valign="top"><a id="a3d98a09e4ccd8bda66cb09a72adaf1fc"></a>
read_id_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">query_read_id_</a></td></tr>
<tr class="memdesc:a3d98a09e4ccd8bda66cb09a72adaf1fc"><td class="mdescLeft">&#160;</td><td class="mdescRight">internal read ID for query <br /></td></tr>
<tr class="separator:a3d98a09e4ccd8bda66cb09a72adaf1fc"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6d01fc190b1cba1c6b41cd89d672b032"><td class="memItemLeft" align="right" valign="top"><a id="a6d01fc190b1cba1c6b41cd89d672b032"></a>
read_id_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">target_read_id_</a></td></tr>
<tr class="memdesc:a6d01fc190b1cba1c6b41cd89d672b032"><td class="mdescLeft">&#160;</td><td class="mdescRight">internal read ID for target <br /></td></tr>
<tr class="separator:a6d01fc190b1cba1c6b41cd89d672b032"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aef98d06e839295136d197fee76feb95e"><td class="memItemLeft" align="right" valign="top"><a id="aef98d06e839295136d197fee76feb95e"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">query_start_position_in_read_</a></td></tr>
<tr class="memdesc:aef98d06e839295136d197fee76feb95e"><td class="mdescLeft">&#160;</td><td class="mdescRight">start position in the query <br /></td></tr>
<tr class="separator:aef98d06e839295136d197fee76feb95e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a03cb25f83ca6344ad1b4108c1d910f0c"><td class="memItemLeft" align="right" valign="top"><a id="a03cb25f83ca6344ad1b4108c1d910f0c"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">target_start_position_in_read_</a></td></tr>
<tr class="memdesc:a03cb25f83ca6344ad1b4108c1d910f0c"><td class="mdescLeft">&#160;</td><td class="mdescRight">start position in the target <br /></td></tr>
<tr class="separator:a03cb25f83ca6344ad1b4108c1d910f0c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a20866810acf35523e87efcb66181a224"><td class="memItemLeft" align="right" valign="top"><a id="a20866810acf35523e87efcb66181a224"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">query_end_position_in_read_</a></td></tr>
<tr class="memdesc:a20866810acf35523e87efcb66181a224"><td class="mdescLeft">&#160;</td><td class="mdescRight">end position in the query <br /></td></tr>
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<tr class="memitem:ad4721b3555a83acb588c54dc369f7797"><td class="memItemLeft" align="right" valign="top"><a id="ad4721b3555a83acb588c54dc369f7797"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">target_end_position_in_read_</a></td></tr>
<tr class="memdesc:ad4721b3555a83acb588c54dc369f7797"><td class="mdescLeft">&#160;</td><td class="mdescRight">end position in the target <br /></td></tr>
<tr class="separator:ad4721b3555a83acb588c54dc369f7797"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7d37018aff3304bbe75b2d612b55c057"><td class="memItemLeft" align="right" valign="top"><a id="a7d37018aff3304bbe75b2d612b55c057"></a>
char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">query_read_name_</a> = 0</td></tr>
<tr class="memdesc:a7d37018aff3304bbe75b2d612b55c057"><td class="mdescLeft">&#160;</td><td class="mdescRight">query read name (e.g from FASTA) <br /></td></tr>
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<tr class="memitem:afcb7e39abf2761899ff1abb3c95b82ca"><td class="memItemLeft" align="right" valign="top"><a id="afcb7e39abf2761899ff1abb3c95b82ca"></a>
char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">target_read_name_</a> = 0</td></tr>
<tr class="memdesc:afcb7e39abf2761899ff1abb3c95b82ca"><td class="mdescLeft">&#160;</td><td class="mdescRight">target read name (e.g from FASTA) <br /></td></tr>
<tr class="separator:afcb7e39abf2761899ff1abb3c95b82ca"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1c0b9bac9b2e15f70c60fcdae9728fd7"><td class="memItemLeft" align="right" valign="top"><a id="a1c0b9bac9b2e15f70c60fcdae9728fd7"></a>
RelativeStrand&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">relative_strand</a></td></tr>
<tr class="memdesc:a1c0b9bac9b2e15f70c60fcdae9728fd7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Relative strand: Forward ("+") or Reverse("-") <br /></td></tr>
<tr class="separator:a1c0b9bac9b2e15f70c60fcdae9728fd7"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab3594748a49ae4472ca28a03b05ddb7d"><td class="memItemLeft" align="right" valign="top"><a id="ab3594748a49ae4472ca28a03b05ddb7d"></a>
std::uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">num_residues_</a> = 0</td></tr>
<tr class="memdesc:ab3594748a49ae4472ca28a03b05ddb7d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Number of residues (e.g anchors) between the two reads. <br /></td></tr>
<tr class="separator:ab3594748a49ae4472ca28a03b05ddb7d"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7677cc8d0aa20fc788b57f85905e051b"><td class="memItemLeft" align="right" valign="top"><a id="a7677cc8d0aa20fc788b57f85905e051b"></a>
std::uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">query_length_</a> = 0</td></tr>
<tr class="memdesc:a7677cc8d0aa20fc788b57f85905e051b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Length of query sequence. <br /></td></tr>
<tr class="separator:a7677cc8d0aa20fc788b57f85905e051b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a2da1b559c8e45c6bc48eda8b60e40c11"><td class="memItemLeft" align="right" valign="top"><a id="a2da1b559c8e45c6bc48eda8b60e40c11"></a>
std::uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">target_length_</a> = 0</td></tr>
<tr class="memdesc:a2da1b559c8e45c6bc48eda8b60e40c11"><td class="mdescLeft">&#160;</td><td class="mdescRight">Length of target sequence. <br /></td></tr>
<tr class="separator:a2da1b559c8e45c6bc48eda8b60e40c11"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a31d4f58b24a2e3fc57b5bca803827360"><td class="memItemLeft" align="right" valign="top"><a id="a31d4f58b24a2e3fc57b5bca803827360"></a>
bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">overlap_complete</a> = false</td></tr>
<tr class="memdesc:a31d4f58b24a2e3fc57b5bca803827360"><td class="mdescLeft">&#160;</td><td class="mdescRight">Whether the overlap is considered valid by the generating overlapper. <br /></td></tr>
<tr class="separator:a31d4f58b24a2e3fc57b5bca803827360"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad9b3ed3f91b4979afb6198cea2d77e54"><td class="memItemLeft" align="right" valign="top"><a id="ad9b3ed3f91b4979afb6198cea2d77e54"></a>
char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">cigar_</a> = 0</td></tr>
<tr class="memdesc:ad9b3ed3f91b4979afb6198cea2d77e54"><td class="mdescLeft">&#160;</td><td class="mdescRight">CIGAR string for alignment of mapped section. <br /></td></tr>
<tr class="separator:ad9b3ed3f91b4979afb6198cea2d77e54"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> - represents one overlap between two substrings</p>
<p><a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> is a region of two strings which is considered to be the same underlying biological sequence. The overlapping region need not be identical across both substrings. </p>
</div><hr/>The documentation for this struct was generated from the following file:<ul>
<li>cudamapper/include/claragenomics/cudamapper/<a class="el" href="types_8hpp_source.html">types.hpp</a></li>
</ul>
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